Mercurial > repos > recetox > ramclustr_csv

annotate ramclustr_csv.xml @ 1:d9c9ec0e2bd8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 36ea15ec5b1f1899f28c3a92d3a55dd6ac3dffae"
author recetox
date Wed, 13 Jan 2021 11:42:34 +0000
parents 43b60b28ccf7
children 08b09930cd73
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
1 <tool id="ramclustr_csv" name="RAMClustR (CSV)" version="@TOOL_VERSION@+galaxy0">
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
2 <macros>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
3 <import>ramclustr_macros.xml</import>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
4 </macros>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
5
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
6 <requirements>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
7 <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
8 </requirements>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
9
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
10 <inputs>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
11 <expand macro="parameters_csv" />
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
12 <expand macro="parameters_required" />
1
d9c9ec0e2bd8 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 36ea15ec5b1f1899f28c3a92d3a55dd6ac3dffae"
recetox
parents: 0
diff changeset
13 <expand macro="parameters_optional_csv" />
0
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
14 </inputs>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
15
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
16 <command detect_errors="aggressive"><![CDATA[
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
17 Rscript
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
18 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
19 -e 'x <- ramclustr_csv(
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
20 ms="$ms_csv.ms",
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
21 idmsms="$ms_csv.idmsms",
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
22 feature_delimiter="$ms_csv.feature_delimiter",
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
23 sample_name_column = $ms_csv.sample_name_column,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
24 retention_time_column= $ms_csv.retention_time_column,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
25 sr = $required.sr,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
26 deep_split = $required.deepSplit,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
27 block_size = $required.blocksize,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
28 mult = $required.mult,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
29 hmax = $required.hmax,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
30 collapse = $required.collapse,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
31 use_pheno = $required.usePheno,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
32 qc_inj_range = $required.qc_inj_range,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
33 normalize = "$required.normalize",
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
34 min_module_size = $required.minModuleSize,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
35 linkage = "$required.linkage",
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
36 mzdec = $required.mzdec,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
37 cor_method = "$required.cor_method",
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
38 rt_only_low_n = $required.rt_only_low_n,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
39 replace_zeros = $required.replace_zeros,
1
d9c9ec0e2bd8 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 36ea15ec5b1f1899f28c3a92d3a55dd6ac3dffae"
recetox
parents: 0
diff changeset
40 st = $ms_csv.st,
0
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
41 #if $optional.maxt
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
42 maxt = $optional.maxt,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
43 #end if
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
44 #if $optional.fftempdir
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
45 fftempdir = $optional.fftempdir,
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
46 #end if
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
47 )'
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
48 -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")'
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
49
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
50 ]]>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
51 </command>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
52
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
53 <outputs>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
54 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
55 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
56 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
57 <expand macro="output_msp"/>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
58 </outputs>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
59
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
60 <help>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
61 Documentation
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
62 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
63
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
64 Upstream Tools
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
65 +-------+------------------------+--------+------------+
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
66 | Name | Output File | Format | Parameter |
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
67 +=======+========================+========+============+
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
68 | ??? | Feature Table with MS1 | csv | ms |
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
69 +-------+------------------------+--------+------------+
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
70 | ??? | Feature Table with MS2 | csv | idmsms |
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
71 +-------+------------------------+--------+------------+
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
72
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
73 The tool takes a **csv** table as input which has to fulfill the following requirements
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
74
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
75 (1) no more than one sample (or file) name column and one feature name row;
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
76 (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
77 (3) features in columns and samples in rows.
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
78
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
79 Downstream Tools
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
80 +---------+--------------+----------------------+
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
81 | Name | Output File | Format |
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
82 +=========+==============+======================+
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
83 | matchMS | Mass Spectra | collection (tgz/msp) |
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
84 +---------+--------------+----------------------+
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
85
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
86 @GENERAL_HELP@
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
87 </help>
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
88
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
89 <expand macro="citations" />
43b60b28ccf7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 12025c9247a7bd1afc327134623c6ae3e048fca8"
recetox
parents:
diff changeset
90 </tool>